All About Gut Bacteria, Symbiosis and Human Health!

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I’ve been working on rewriting my book description, as I’ve never liked the one I used. So, today’s post is all about updates on TSF. I’m working on the next book too, and it’s all about applying the information from TSF to everyday life! So, here’s the update so far, with a linky at the bottom:

What if many of the things you thought you knew about being human did not actually work the way you were taught?

What if scientific research into gut bacteria had revealed huge amounts of information about their role in human function, health, emotions and appetite and healthcare hadn’t caught up at all?

What if you could find out the key to controlling your weight without starving yourself or undergoing dangerous surgery?

What if the book you’re looking at could teach you about the explosion of scientific research on the microbiome, without you having to read a few thousand studies to understand it?

You’ve probably heard that our gut bacteria vastly outnumber our human cells, and our gut bacteria’s gene pool includes more than one hundred times the gene count as our human cells. What does that mean and how does it work?

If you’re interested in knowing more about “what makes us tick” physically and emotionally, how to hurt less and age more gracefully, then this book is for you!

If you’re tired of books that state the author’s opinion or make broad claims without scientific backing or support, this book includes about 1300 peer-reviewed research studies, and the e-book has links to those studies on the National Library of Health/National Library of Medicine.

One of the inspirations for this book was research published by the late Prof. Eshel Ben-Jacob, a brilliant Israeli researcher. I was able to share this book with him before he passed away, and this is what he said about it:

“This excellent and long needed book presents in a clear and sound manner the recent dramatic findings about our gut bacteria. These thousands of trillions microorganisms living inside us play a crucial role in regulating our well-being throughout life. The new message is of great importance to the entire medical community, life sciences researchers, as well as the general public. Realizing the role of gut bacteria can help each of us to better understand the effect of nutrients, as mediated by the gut bacteria, on our body in health, in disease and in special times, such as pregnancy, nursing or periods of high stress. For example, we now understand that the massive use of antibiotics in children, adults and agriculture has endangered our vital microbiome and is liable to cause diseases such as Type 2 diabetes on a global scale. The gut microbiome is emerging as a vital part of humanity, without which health and happiness are severely compromised. The time has come for this knowledge to be widely understood!”

Professor Eshel Ben-Jacob, International member of the American Philosophical Society

Professor of Physics
The Maguy-Glass Professor
in Physics of Complex Systems
School of Physics and Astronomy
Tel Aviv University, 69978 Tel Aviv, Israel

What are the causes of dysbiosis and resultant dysfunction/disease? One cause that seems to be greatly underestimated may be simply our mood! Human beings, having been gifted with large frontal lobes, are capable of experiencing and expressing a variety of moods. Our bodies respond to these moods with different functional states, some of which have been categorized. These are “fight or flight (or sometimes, fight/flee/fortify)” or “wine and dine”. There are many more physiological functional arousal states that we could elaborate on, but many of them could make this blog post NSFW. We’ll just assume that your imagination can fill in the blanks with how the body responds to the mind! With the brain-gut connection in mind, and being also cognizant that it’s a two-way street since the gut influences the brain, what would be the influence of stress? One that comes to mind right away is a reduction in gut motility. This changes the environment in which the microbiome exists, and will change the demographics of the microorganisms. What about the effects of peristalsis on the small intestine? If there is less peristalsis, wouldn’t it make it easier for colonic organisms to migrate to the small intestine? If transit times increase, different stages of food digestion could release different nutrients, feeding different organisms. When do we cross from fermentative to putrefactive dominance? Using one of the concepts in The Symbiont Factor, this two-way function of gut/brain/gut axis can cause a positive feedback loop. If gut organisms that flourish during emotional stress can also alter neurotransmitter function at the brain, wouldn’t that predispose the brain to perceive stress following stressful events? What if that is why sometimes after a stressful day we just have more stress, no matter what happens? It is as if our very perception of our environment is vulnerable to plasticity. If this is allowed to happen without our conscious intervention (things like deciding to meditate or do some yoga even though you’re angry) the combination of evoked brain plasticity with gut symbiont evolution could be what makes it hard to shake off stress! Ironically, this same plasticity is probably an evolutionary advantage, allowing genetic selection of the microbiome on an ongoing real-time basis to adapt to circumstances. The problem is that our modern circumstances provide constant chemical and emotional pressure to this system, resulting in “learned dysfunction” of both the gut and the brain! This highlights the importance of “mental housekeeping” and lifestyle choices in determining our “perceptual future”. If you don’t want the world to seem as stressful, start taking care of mind, body, and symbiont health!

The Problem with RoundUp and its health effects
Sometimes during a debate it becomes obvious that one side is simply not telling the truth. Such seems to be the case when considering RoundUp, currently still promoted as the safest herbicide ever produced. It is also the most commonly used, with a recorded 187 million pounds used by US farmers in 2007. More current usage is not known, but estimated at over 200 million pounds in the US. The maker of RoundUp, Monsanto, continues to maintain that it is nontoxic and completely safe. This belief permeates to those who use it, with readers offering comments at the end of the article defending its safety. Most homeowners use RoundUp to control weeds, and most farmers use it liberally on crops. This is possible because of genetic modification of crops to permit resistance to glyphosate, permitting the killing of weeds without killing the crop. Recently articles have been published online suggesting that the problem with wheat causing celiac disease or gluten sensitivity has more to do with residual levels of glyphosate than with gluten content. The suggestion that pre-harvest spraying of crops with glyphosate to reduce weed content, promote dessication and improve yield is typically met with a hailstorm of accusations of “pseudoscience” and “fearmongering.” There are usually some vehement denials that pre-harvest spraying is ever carried out. An example of one such article can be found here: http://tinyurl.com/n9rtzpn

With this in mind let us consider two questions: Is glyphosate toxic, and are crops really sprayed prior to harvest?

The reason that glyphosate is “considered safe” is that it inhibits a metabolic pathway in plants known as the Shikimate pathway. This inhibition interrupts the plant’s metabolism and kills it. Humans and other eukaryotic species do not have a Shikimate pathway, and so the claim of safety appears to be scientifically sound…or is it? All eukaryotic organisms including humans have cellular power-producing structures known as mitochondria. These structures are where energy is produced so that the cell and the organism have fuel. Mitochondria, however, are really not of human origin. Thought to be the end result of ancient indwelling symbionts (endosymbiont theory if you’d like to look that up) mitochondria are more similar to bacteria than human cells. Their DNA is circular, just as bacterial DNA is circular. This isn’t some new discovery as geneticists have been using this mitochondrial DNA to track the human family tree for years. You see, mitochondrial DNA is matrilineal-it is only inherited from the mother, not from the father. This provides a unique opportunity to track one side of the family tree more accurately than is possible with human DNA. It’s also the first clue to glyphosate’s toxicity, as bacteria have a Shikimate pathway! Predictably mitochondria also have a Shikimate pathway. There is already a research paper stating this (Mesnage, Seneff). There is also an effect in the microbiome, as glyphosate is more toxic to some microorganisms than to others, causing an imbalance in this critical ecosystem. Kruger found that glyphosate reduced the inhibition of Clostridium (a pathogen) by Enterococcus species, causing imbalance and disease. A differential toxic effect was found in chickens by Shehata, who showed the glyphosate inibited beneficial microbial species yet did not inhibit pathogenic ones. Changes in gut bacteria in humans can alter serotonin levels, affecting behavior, mood and susceptibility to brain trauma (Morley). The microbiome living in our intestines are critical to our health and are vulnerable to changes in intestinal function (Matthews). It has been found that at very dilute concentrations, far less than commercial farming uses, glyphosate reduces intestinal motility (Chlopecka). This would result in more constipation, dramatic shifts in population dynamics and an increased risk of small intestinal bacterial overgrowth (SIBO) due to reduced motility allowing contents of the colon to move into the small intestine. Glyphosate has been found to trigger pathways producing cellular apoptosis (think cell sepuku) and increased reactive oxygen species producing damaging oxidation (Chaufan).
There is always someone who, in the comments following an article critical of Roundup, offers to drink a glass of it to prove its safety. This is ill advised, as glyphosate is far from nontoxic. Instead, it has been found to produce respiratory depression, bradycardia (so, you can’t breathe and your heart slows), acidosis, hyperkalemia, cardiac block or arrythmia and death. Hemodialysis and intubation are required to help the patient survive, as there is no antidote to glyphosate poisoning (Garlich, Gress).

You might notice that many of these organizations providing pre-harvest spraying guidelines are university agricultural programs. If you’re not familiar with ag programs, you might even wonder why they would recommend such a practice in light of the research information on glyphosate’s biologic effects (and there are many more articles showing its effects; I didn’t even scratch the surface really!). The old adage of “follow the money” could never be more accurate: http://tinyurl.com/mhyvwzy, http://tinyurl.com/ctw2aq7 as the codependent relationship that has evolved between Monsanto and institutes of higher education is both diabolically brilliant and nauseatingly common.

If you needed more reasons to shop for organically grown fruits and vegetables or use grains other than wheat, you now have them. If you think just avoiding wheat will solve the problem, consider that the same recommendations exist for barley, oats, flax, canola, peas, lentils, soybeans and dried beans (page 31 of http://tinyurl.com/q2o8f96 lists all of these as recommendations for pre-harvest spraying in Canada, and others list ‘small grains’ in the guidelines: http://tinyurl.com/o994mk2).

We have arrived at a time in history when the business interests of corporate entities often take precedence over the health needs of society’s human members. When we allow large corporations to control what is taught in schools and what guidelines are imposed by government, we can count on one thing-being counted out of the deal.

After a year and a half of having a second job as a new author, my first book is finally available in print! A comprehensive, thoroughly referenced guide to how our gut bacteria influence physical and mental health: The Symbiont Factor is now available on Amazon as a paperback! If you ever wondered if and why probiotics are healthy you should read this book. Please share with your contacts 🙂 http://tinyurl.com/pe2g4xt

Today is the day I finally got to click on the “submit” button and make my book available on Amazon. After a year of hard work writing and making edit corrections, it’s done! A print copy will be available soon-for now only the e-book version is available.

Kefir is a fermented milk product with at least a two millenium history of human use. Native people such as the Maasai have used fermentation to preserve their milk products. Kefir is the most popular fermented dairy product in Russia and is thought to have originated in the Caucasus mountain region. Milk that is fermented into kefir has been found to last at least six weeks in refrigeration with no spoilage or loss of probiotic organisms! This is significantly longer than pasteurized and unfermented milk, and works the same way whether with camel, cow, goat or sheep’s milk. Kefir has been found to have many health benefits, among them:

-Kills drug-resistant myeloid leukemia cells

-Slows the progression of kidney disease

-Improves fatty liver disease

-Reduces obesity/body fat content

So, how do you make your own? It’s really simple, actually! All you need is milk, a starter culture, and a jar. Starter cultures can be obtained from someone else who is making kefir, or started from commercially available packets:

The culture that ferments kefir is known as a SCOBY, or symbiotic culture of bacteria and yeast. Over time, this culture will grow until it looks a bit like soggy cauliflower:

If making kefir for the first time using a package mix, it is best to follow the directions provided with the kefir grains. When you strain out the grains as shown above, they will grow over time and form a bigger SCOBY. This SCOBY is fairly advanced-it’s a good time to share with someone else! This one can ferment a quart of milk into kefir in 24 hours.

The first step to making kefir from a SCOBY is to add the SCOBY to the fermenting vessel (fancy word for quart mason jar in this case!)

The next step is to add the milk:

Then cover the top with a coffee filter or paper towel, to keep dust and insects from contaminating your kefir culture.

and use either a rubber band or one of the threaded rings (since this is a canning jar) to keep the filter attached tightly:

At this point, I place the jar on top of my refrigerator.

It works best if you take it down and stir it lightly 2-3x/day, or at least give it a good swirling-about, to distribute the bacteria more evenly in the milk. If you prefer a lighter fermentation, 24 hours may be sufficient. I prefer a thicker, stronger fermentation, and often leave it 48 hours or place it in the refrigerator the last 24 hours before removing the SCOBY. The next step is to strain out the SCOBY:

The SCOBY culture can then be put into a smaller glass jar with some fresh milk and stored in the refrigerator, or the process can be repeated to start the next batch of kefir. Using this information, you can create your own healthy kefir at home! We use goat milk obtained from a local farm, but it will work with other types of milk or store-bought goat milk also. Fermentation of milk in this manner preserves the milk, as the bacterial culture will actively inhibit or kill any invading bacteria that might cause spoilage or disease. It has been shown to last at least six weeks, as mentioned above. Will pasteurized milk last six weeks if not fermented? Hardly-it would be a horrid stinking mess! In the same manner, unfermented milk that is fermented is safer for consumption than pasteurized milk that is unfermented. Once finished, kefir can be enjoyed as-is, blended with fruit to make smoothies, or added to other drinks and dishes. So get started and enjoy this healthy probiotic beverage!

The last decade of research has advanced the understanding of life itself to such a degree that our definitions of “life” must now be adjusted. Until now, you may have regarded yourself as a singular entity; a “human being,” a “person” or just “me.” All of these terms indicate a belief system grounded in what is now an outdated concept. What if we were actually a cooperative group of organisms existing together for mutual benefit? Trillions of organisms, all sharing physical space and each contributing to the functioning of the whole. What if even our very consciousness were not a singular thing or the result of one personality, but more of a democratic/summative system or even a type of hive consciousness? All of these are functional realities to one extent or another. Oh, and one more thing…those human cells? They are in the minority and are outnumbered at least 10:1. Well, you might be thinking, a human being is defined by a specific genetic code, 23 pairs of chromosomes, a little over 21,000 genes that code for everything we are, right? Not so fast! Genes do encode for the protein molecules that carry out life functions, but if a person were to develop with only those 21,000 genes the brain, nervous system, immune system, endocrine and digestive systems would not develop or function normally at all. So where does all the other information come from?

“We” are an organism that includes several trillion symbiont organisms that all contribute genes. In fact, looking at a person from head to toe genetically reveals that the human genes are only 1/100th, or 1 percent, of the genes present. The majority of the remaining genome is bacterial in origin. We are only 1% or less human from a genetic standpoint! Scientists and researchers now know that the human body depends on this bacterial genetic reservoir of information for normal development and function. The human immune system, for example, is cultivated by the bacteria and “taught” how to function, what to kill and what to tolerate. Without this ancient genetic wisdom (bacteria have existed for an estimated 2 billion years) the human immune system does not function normally. Our brain is no different; without bacterial symbiont assistance the human brain is emotionally and functionally unstable. The result is an inflamed brain, anxiety and depression or schizophrenia, and an increased likelyhood of neurodegenerative diseases such as Parkinson’s, Alzheimer’s, or neuroimmune conditions such as Multiple Sclerosis. The digestive tract would not function normally either! Even our mind, that last refuge of a singular “self,” is not the result of a singular organism’s activities. Dominant colonies of bacteria wield significant influence on our mood, decision making and basic personality. Our appetite for specific food items as well as our overall appetite is heavily influenced by gut bacteria. Neurotransmitters that determine mood are both produced and consumed by the gut bacteria, exerting influence over mood. Neurotransmitter receptor sites in various specific areas of the human brain are sensitized or desensitized by symbiont bacteria. The result is a distinctly different emotional profile and personality! It is truly the result of the interactions of many organisms.
Our human parts in turn “farm” these bacterial colonies to keep them viable and performing their needed tasks.

The terms that have been coined for these concepts refer to “us” as Holobionts-a host plus its symbionts form the organism we call “human.” The total gene pool within the holobiont is called the Hologenome. All other eukaryotic life is thought to exist on the same principle of cooperative function between host and symbionts. The bacterial symbionts are capable of influencing mate choice, reproductive success and driving speciation to create new species from existing ones (really.)

After re-reading the previous discussion, you might be incredulous that life itself has been essentially redefined, and yet it did not really result in significant changes in healthcare practices. This is perhaps the most promising yet overlooked, proven yet controversial new development in decades. Healthcare is replete with legions of “singular organism, flat-earth-society” members who are slow to accept this new concept despite its promise of more effective interventions. As examples of the conflicts in logic that result, consider the following questions-each of which may be the subject of another blog post and are written of in The Symbiont Factor.

-If the body is dependent on symbiont bacteria for normal function, what is the result of taking antibiotics?
-If antibiotics are added to our food, what is the effect on our own personal hologenome?
-If food is routinely disinfected, what is the effect on hologenomic diversity?
-What are the long-term consequences of bacteria sharing plasmids (DNA fragments) that code for antibiotic resistance?
-If symbiont bacteria maintain immune system function, why do we kill them in cases of infection or cancer, when the immune system is needed the most?
-If so much physical and mental function depend on gut bacteria, why do we not evaluate the gut bacteria when something seems physically or mentally dysfunctional?
-Where do all of these symbiont bacteria come from in the environment?
-What is the effect of chemical environmental pollution on the potential microbiome?
-How does nutrition affect their population demographics?
-If two people have differing microbiomes, would a given medication affect them differently?
-Do different birthing and childcare practices affect the hologenomic outcome?
-If the bacterial symbionts have such an influence on human emotion and personality, why is this not addressed in psychology and psychiatry practice?
-How does being a holobiont with such a diverse colony of bacteria provide an evolutionary or competitive advantage?

As we move forward into the 21st century, we must strive to add holobiont concepts to the practice of healthcare and teach individuals why “taking care of yourself” might need to become “taking care of each other.” Perhaps better pollution control, for example, would be more meaningful if people understood that it isn’t only to save some small toad that lives far away, but also to save the bacterial diversity that our future depends on. Perhaps parenting practices would mean more when the importance of imparting a beneficial microbiome/hologenome to our children is better understood. These concepts form the basis for The Symbiont Factor, referenced with more than 1300 peer-reviewed research papers and due to be published by 15 June 2014.